- <li><em><font size="3">JVL file</font></em>
- <p>
- The easiest way to launch Jalview with a different percentage of physical memory available is to
- create a text file with extension <em>.jvl</em> and with content that contains the line
- <pre>
- jalview.jvmmempc=50
- </pre>
- Replace the value with the percentage of memory you wish to allocate to Jalview.
- </p>
- <p>
- In Windows and in macOS you can then launch Jalview by double clicking on this file, and your memory setting will be used instead of the default value of 90.
- </p>
- <p>
- In Linux or other unix variants you can launch Jalview on the command line and provide your JVL file as an argument with
- <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl
- </pre>
-
- </p>
- <p>
- If you want to use a memory setting like this and open a file you can use both the jvl and alignment files as command line arguments, but you must put the <em>jvl</em> file first, e.g.
- <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa
- </pre>
- alternatively, you can use the standard Jalview command line arguments with or without the jvl file (first), e.g.
- <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
- </pre>
- </p>
-
- <p>
- You can use command line arguments to control memory settings in Windows and macOS too:
- <br/>
- In Windows you must use, e.g.
- <pre>
- \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa
- </pre>
- and in macOS you can use the macOS <em>open</em> command like this:
- <pre>
- open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa
- </pre>
- (put all the Jalview arguments <em>after</em> the --args parameter).
-
- </p>
- </li>
-
-
- <li><em><font size="3">Directly opening Jalview with a JVM</font></em>
- <p>
- Launching Jalview directly with a JVM is entirely possible, but is not recommended as automatic updates and some other default settings will not operate.
- </p>
- <p>
- However by launching Jalview in this way you have full access to the Java command line arguments.
- In particular you can set the maximum allowed memory with the <em>-Xmx...</em> JVM argument.
- <br/>
- <em>-Xmx</em> should be immediately followed (no space or equals) by the maximum amount of memory that you might want to launch Jalview with. This can be specified in bytes as just a number,
- or in kilobytes, megabytes or gigabytes by following the number with a "k", "m" or "g" respectively. e.g.
- <pre>
- -Xmx8g
- </pre>
- </p>
- <p>
- Jalview binaries for Windows and macOS are distributed with their own JVM which you will find in
+ <li><em><font size="3">JVL file</font></em> <br /> The easiest
+ way to launch Jalview with a different percentage of physical
+ memory available is to create a text file with extension <em>.jvl</em>
+ and a single line to specify the percentage of memory you wish
+ Jalview to request: <pre>
+ jalview.jvmmempc=50</pre> In Windows and in macOS you can then launch Jalview by
+ double clicking on this file, and your memory setting will be used
+ instead of the default value. <br /> <br /> In Linux or other
+ unix variants you can launch Jalview on the command line and
+ provide your JVL file as an argument with <pre>
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl</pre> If you want to use a memory setting like this and open a
+ file you can use both the jvl and alignment files as command line
+ arguments, but you must put the <em>jvl</em> file first, e.g. <pre>
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
+ arguments with or without the jvl file (first), e.g. <pre>
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
+ settings in Windows and macOS too: <br /> In Windows you must
+ use, e.g. <pre>
+ \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre> In macOS you can use the macOS <em>open</em> command like this: <pre>
+ open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa</pre><em>(put all the Jalview arguments <em>after</em> the --args
+ parameter)
+ </em><br/><br/></li>
+ <li><em><font size="3"><a name="jvm"/>Directly opening Jalview
+ with a JVM</font></em> <br /> Launching Jalview directly with a JVM is
+ entirely possible, but is not recommended for regular interactive
+ use because it bypasses Jalview's launcher which also handles
+ automatic updates and configuration of other aspects of Jalview
+ operation. <br /> However by launching Jalview in this way you
+ have full access to the Java command line arguments. In particular
+ you can set the maximum allowed memory with the <em>-Xmx...</em>
+ JVM argument. <br /> <em>-Xmx</em> should be immediately followed
+ (no space or equals) by the maximum amount of memory specified in
+ bytes, or in kilobytes, megabytes or gigabytes by following the
+ number with a "k", "m" or "g" respectively. <br />For example: <pre>
+ -Xmx8g</pre>Jalview binaries for Windows and macOS are distributed
+ with their own JVM which you will find in
+ <ul>
+ <li><em>Windows:</em> .../Jalview/jre/bin/java.exe</li>
+ <li><em>macOS:</em>
+ .../Jalview.app/Contents/Resources/app/jre/Contents/Home/bin/java</li>
+ </ul> For linux and other unixes you will have to install a Java 1.8
+ JRE (we recommend the ones found at <a
+ href="https://adoptopenjdk.net">https://adoptopenjdk.net/</a>) <br />
+ <br /> You will also need to reference the "appdir" release
+ folder with all of the Jalview jar files.